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Tam NT, Nhan DK. Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:358. [PMID: 38785840 PMCID: PMC11117668 DOI: 10.3390/biology13050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
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Affiliation(s)
- Nguyen Thanh Tam
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
| | - Dang Kieu Nhan
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
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Liu G, Li Y, Sun X, Guo X, Jiang N, Fang Y, Chen J, Bao Z, Ma F. Association study of SNP locus for color related traits in herbaceous peony ( Paeonia lactiflora Pall.) using SLAF-seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1032449. [PMID: 36544869 PMCID: PMC9760751 DOI: 10.3389/fpls.2022.1032449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs.
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Affiliation(s)
- Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Ying Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xia Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xianfeng Guo
- College of Forestry, Shandong Agricultural University, Tai-An, Shandong, China
| | - Nannan Jiang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Yifu Fang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Junqiang Chen
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
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Liu Z, Zeng Z, Yang X, Zhu S, Liu T, Wang Y. Genetic insights into the crude protein and fiber content of ramie leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:969820. [PMID: 36267946 PMCID: PMC9577236 DOI: 10.3389/fpls.2022.969820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Ramie (Boehmeria nivea L.) is a perennial plant with vigorously vegetative growth and high nutritive value that is an excellent source of green feed in China. Crude protein and fiber content are the most important traits associated with ramie forage quality; however, their genetic basis remains largely unknown. In this study, we investigated the genetic architecture of these two traits using an F2 population derived from cultivated Zhongsizhu 1 (ZSZ1) and wild Boehmeria nivea var. tenacissima (tenacissima). Linkage mapping identified eight quantitative trait loci (QTLs) in crude fiber and one QTL in crude protein. Of these, five were further validated by association analysis. Then, two major QTLs for crude fiber content, CF7 and CF13, were further identified using bulked segregant analysis (BSA) sequencing, and their exact physical intervals were determined via genotype analysis of F2 progenies with extremely low crude fiber content. In total, 10 genes in the CF7 and CF13 regions showed differential expression in ZSZ1 and tenacissima leaves, including an MYB gene whole_GLEAN_10016511 from the CF13 region. Wide variation was observed in the promoter regions of whole_GLEAN_10016511, likely responsible for its downregulated expression in tenacissima. Interestingly, more fiber cells were observed in Arabidopsis with overexpression of whole_GLEAN_10016511, indicating that the downregulated expression of this gene could have an association with the relatively low fiber content in wild tenacissima. These results provided evidence that whole_GLEAN_10016511 is a logical candidate for CF13. This study provides important insights into the genetic basis underlying ramie crude protein and fiber content, and it presents genetic loci for improving the forage quality of ramie using marker-assisted selection.
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Affiliation(s)
- Zhiyong Liu
- College of Agriculture, Yangtze University, Jingzhou, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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Bai X, Wang X, Wang Y, Wei Y, Fu Y, Rao J, Ma Y, Zeng Z, Li F, Wang M, Zhu S. Genome-Wide Association Study of Six Forage Traits in Ramie ( Boehmeria nivea L. Gaud). PLANTS (BASEL, SWITZERLAND) 2022; 11:1443. [PMID: 35684216 PMCID: PMC9182863 DOI: 10.3390/plants11111443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association study (GWAS) of six forage traits using whole-genome sequencing data generated from 301 ramie accessions found that traits were continuously distributed; the maximum variant coefficient was fresh weight per clump (FWPC) (2019) and individual plant height (IPH) (2019) minimum. Correlation analysis demonstrated that 2019 and 2020 results were similar; all traits were correlated. GWAS analysis demonstrated that six traits exhibited consistent and precise association signals. Of the latter, 104 were significant and detected in 43 genomic regions. By screening forage trait-associated single nucleotide polymorphisms and combining Manhattan map with genome annotation, signals were categorized according to functional annotations. One loci associated with fresh weight per plant (FWP) (chromosome 5; Bnt05G007759), two associated with FWPC (chromosome 13; Bnt13G018582, and Bnt13G018583), and two associated with leaf dry weight per plant (LDWP) and dry weight per plant (DWP) (chromosome 4; Bnt04G005779 and Bnt04G005780), were identified. We describe forage trait candidate genes that are highly correlated with FWP and FWPC; Bnt05G007759 may be involved in nitrogen metabolism, while Bnt13G018582 and Bnt13G018583 may encode TEOSINTE branch 1/CYCLOIDEA/proliferating cytokine 1 (TCP) domains. Bnt04G005779 and Bnt04G005780, which may regulate growth and development, are highly related to LDWP and DWP. These genomic resources will provide a basis for breeding varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Siyuan Zhu
- Correspondence: ; Tel.: +86-138-7580-0740
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Zeng Z, Zhu S, Wang Y, Bai X, Liu C, Chen J, Zhang T, Wei Y, Li F, Bao Z, Yan L, Wang H, Liu T. Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:323-334. [PMID: 34558775 PMCID: PMC8753365 DOI: 10.1111/pbi.13714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/13/2021] [Indexed: 05/27/2023]
Abstract
Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Siyuan Zhu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Yanzhou Wang
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Xuehua Bai
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Chan Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Jianrong Chen
- College of Biological and Environmental EngineeringChangsha UniversityChangshaChina
| | - Ting Zhang
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Yiping Wei
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Fu Li
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Zhigui Bao
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Li Yan
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | | | - Touming Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
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Chen K, Guo B, Yu C, Chen P, Chen J, Gao G, Wang X, Zhu A. Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie ( Boehmeria nivea L.). PLANTS 2021; 10:plants10010160. [PMID: 33467608 PMCID: PMC7830346 DOI: 10.3390/plants10010160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022]
Abstract
The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.
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